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Benchmarks for Tools of Logical Models

With the aim to facilitate benchmarking of several methods and tools for logical model analysis, we will assemble a collection of test models, modelling tools and their supported features, as well as a script to measure running time for each combination.

Setup

  1. Tools

    • every tool lives in its own folder, e.g. tools/PyBoolNet/
    • tools/PyBoolNet/config.txt contains infos about the tool, e.g. multivalued: false
    • tools/PyBoolNet/source/ contains Linux source files
    • tools/PyBoolNet/features/ contains a shell script for every benchmark the tool can handle, e.g. tools/PyBoolNet/features/steadystates

  2. Models

    • all models are kept in tools/models/
    • whether a model is boolean or multi-valued is determined by the file extension with bnet for boolean models and sbml for multi-valued models